# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 19:15:02 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: N-methyl-4-{[trans-4-({[4-(trifluoromethoxy)phenyl]carbamoyl}amino)cyclohexyl]oxy}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1ccc(O[C@@H]2CC[C@H](CC2)NC(=O)Nc3ccc(OC(F)(F)F)cc3)cc1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 KC4  KC4  N-methyl-4-{[trans-4-({[4-(trifluoromethoxy)phenyl]carbamoyl}amino)cyclohexyl]oxy}benzamide  ligand  56  32  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KC4
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 KC4  C10  C  CH1   0   0.044   -3.2110  -1.4020   0.2138
 KC4  C13  C  CH1   0  -0.049   -0.2661  -1.4588   0.1876
 KC4  C15  C  C     0   0.741    2.1054  -0.8738  -0.0922
 KC4  C20  C  CR16  0  -0.287    6.7221  -0.4327  -1.6339
 KC4  C21  C  CR6   0   0.289    7.0286   0.5849  -0.7476
 KC4  C28  C  CR16  0  -0.314    4.7613   0.6165   0.0407
 KC4  C01  C  CH3   0  -0.513  -11.3865   1.9619  -0.0867
 KC4  N02  N  NH1   0  -0.645  -10.1670   1.2346   0.1743
 KC4  O04  O  O     0  -0.499   -8.8875   2.5958  -1.0720
 KC4  C05  C  CR6   0  -0.058   -7.7994   0.7881   0.0102
 KC4  C06  C  CR16  0  -0.259   -6.6657   0.8842  -0.7897
 KC4  C07  C  CR16  0  -0.362   -5.5202   0.1529  -0.5204
 KC4  C08  C  CR6   0   0.396   -5.4847  -0.6987   0.5840
 KC4  O09  O  O2    0  -0.489   -4.4417  -1.4661   0.9332
 KC4  C11  C  CH2   0  -0.460   -2.4484  -2.6760   0.5378
 KC4  C12  C  CH2   0  -0.460   -1.0923  -2.6931  -0.1596
 KC4  N14  N  NH1   0  -0.691    0.9928  -1.5102  -0.5271
 KC4  O16  O  O     0  -0.518    2.1760  -0.3001   0.9841
 KC4  N17  N  NH1   0  -0.792    3.1591  -0.9581  -0.9757
 KC4  C18  C  CR6   0   0.386    4.4332  -0.4209  -0.8364
 KC4  C19  C  CR16  0  -0.351    5.4326  -0.9298  -1.6723
 KC4  F24  F  F     0  -0.301    8.8455   0.7398   1.3824
 KC4  F25  F  F     0  -0.301    9.4119  -0.6970  -0.1012
 KC4  F26  F  F     0  -0.278   10.3505   1.2437  -0.0747
 KC4  C27  C  CR16  0  -0.289    6.0564   1.1110   0.0820
 KC4  C29  C  CH2   0  -0.440   -1.0492  -0.1808  -0.1127
 KC4  C30  C  CH2   0  -0.480   -2.3986  -0.1731   0.5999
 KC4  C31  C  CR16  0  -0.341   -6.6118  -0.7885   1.4062
 KC4  C32  C  CR16  0  -0.274   -7.7476  -0.0585   1.1197
 KC4  H1   H  HCH1  0   0.229   -3.4140  -1.3882  -0.8650
 KC4  H2   H  HCH1  0   0.243   -0.0417  -1.4861   1.2572
 KC4  H3   H  HCR6  0   0.281    7.4730  -0.8344  -2.3012
 KC4  H4   H  HCR6  0   0.284    4.0207   1.0525   0.6899
 KC4  H5   H  HCH3  0   0.240  -11.2994   3.0048   0.2173
 KC4  H6   H  HCH3  0   0.236  -11.6616   1.9363  -1.1426
 KC4  H7   H  HCH3  0   0.250  -12.1873   1.5048   0.4874
 KC4  H8   H  HNH1  0   0.409  -10.2403   0.3640   0.6715
 KC4  H9   H  HCR6  0   0.261   -6.6695   1.5418  -1.6488
 KC4  H10  H  HCR6  0   0.279   -4.6715   0.2636  -1.1805
 KC4  H11  H  HCH2  0   0.233   -2.3076  -2.7490   1.6209
 KC4  H12  H  HCH2  0   0.252   -3.0299  -3.5469   0.2285
 KC4  H13  H  HCH2  0   0.228   -1.2395  -2.7409  -1.2448
 KC4  H14  H  HCH2  0   0.254   -0.5476  -3.5956   0.1241
 KC4  H15  H  HNH1  0   0.393    0.9525  -1.8199  -1.4860
 KC4  H16  H  HNH1  0   0.410    3.0460  -1.5798  -1.7623
 KC4  H17  H  HCR6  0   0.278    5.1993  -1.7289  -2.3655
 KC4  H18  H  HCR6  0   0.279    6.2876   1.9276   0.7535
 KC4  H19  H  HCH2  0   0.248   -0.4679   0.6904   0.1945
 KC4  H20  H  HCH2  0   0.224   -1.1987  -0.0968  -1.1945
 KC4  H21  H  HCH2  0   0.253   -2.9335   0.7478   0.3582
 KC4  H22  H  HCH2  0   0.235   -2.2467  -0.1761   1.6841
 KC4  H23  H  HCR6  0   0.268   -6.5865  -1.4344   2.2747
 KC4  H24  H  HCR6  0   0.256   -8.5877  -0.1441   1.7975
 KC4  O22  O  O2    0  -0.524    8.3115   1.1281  -0.7442
 KC4  C03  C  C     0   0.527   -8.9885   1.6154  -0.3418
 KC4  C23  C  CT    0   1.070    9.2040   0.6058   0.1032

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 KC4  C01  N02  single    1.444  0.020  1.444
 KC4  N02  C03  single    1.342  0.020  1.342
 KC4  O04  C03  double    1.227  0.020  1.227
 KC4  C03  C05  single    1.491  0.020  1.491
 KC4  C05  C06  aromatic  1.391  0.020  1.391
 KC4  C05  C32  aromatic  1.397  0.020  1.397
 KC4  C06  C07  aromatic  1.385  0.020  1.385
 KC4  C32  C31  aromatic  1.380  0.020  1.380
 KC4  C07  C08  aromatic  1.395  0.020  1.395
 KC4  C31  C08  aromatic  1.398  0.020  1.398
 KC4  C08  O09  single    1.341  0.020  1.341
 KC4  O09  C10  single    1.427  0.020  1.427
 KC4  C10  C11  single    1.520  0.020  1.520
 KC4  C10  C30  single    1.523  0.020  1.523
 KC4  C11  C12  single    1.525  0.020  1.525
 KC4  C30  C29  single    1.526  0.020  1.526
 KC4  C12  C13  single    1.525  0.020  1.525
 KC4  C29  C13  single    1.529  0.020  1.529
 KC4  C13  N14  single    1.449  0.020  1.449
 KC4  N14  C15  single    1.354  0.020  1.354
 KC4  C15  O16  double    1.222  0.020  1.222
 KC4  C15  N17  single    1.378  0.020  1.378
 KC4  N17  C18  single    1.390  0.020  1.390
 KC4  C28  C18  aromatic  1.397  0.020  1.397
 KC4  C28  C27  aromatic  1.387  0.020  1.387
 KC4  C18  C19  aromatic  1.399  0.020  1.399
 KC4  C27  C21  aromatic  1.382  0.020  1.382
 KC4  F24  C23  single    1.335  0.020  1.335
 KC4  F26  C23  single    1.324  0.020  1.324
 KC4  C19  C20  aromatic  1.383  0.020  1.383
 KC4  C23  O22  single    1.337  0.020  1.337
 KC4  C23  F25  single    1.335  0.020  1.335
 KC4  C21  C20  aromatic  1.384  0.020  1.384
 KC4  C21  O22  single    1.393  0.020  1.393
 KC4  C10  H1   single    0.970  0.020  1.090
 KC4  C13  H2   single    0.970  0.020  1.090
 KC4  C20  H3   single    0.930  0.020  1.080
 KC4  C28  H4   single    0.930  0.020  1.080
 KC4  C01  H5   single    0.970  0.020  1.090
 KC4  C01  H6   single    0.970  0.020  1.090
 KC4  C01  H7   single    0.970  0.020  1.090
 KC4  N02  H8   single    0.860  0.020  1.020
 KC4  C06  H9   single    0.930  0.020  1.080
 KC4  C07  H10  single    0.930  0.020  1.080
 KC4  C11  H11  single    0.970  0.020  1.090
 KC4  C11  H12  single    0.970  0.020  1.090
 KC4  C12  H13  single    0.970  0.020  1.090
 KC4  C12  H14  single    0.970  0.020  1.090
 KC4  N14  H15  single    0.860  0.020  1.020
 KC4  N17  H16  single    0.860  0.020  1.020
 KC4  C19  H17  single    0.930  0.020  1.080
 KC4  C27  H18  single    0.930  0.020  1.080
 KC4  C29  H19  single    0.970  0.020  1.090
 KC4  C29  H20  single    0.970  0.020  1.090
 KC4  C30  H21  single    0.970  0.020  1.090
 KC4  C30  H22  single    0.970  0.020  1.090
 KC4  C31  H23  single    0.930  0.020  1.080
 KC4  C32  H24  single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 KC4  H1   C10  C30  109.73  3.000
 KC4  H1   C10  C11  108.23  3.000
 KC4  C30  C10  C11  110.78  3.000
 KC4  H1   C10  O09  109.67  3.000
 KC4  C30  C10  O09  111.62  3.000
 KC4  C11  C10  O09  106.72  3.000
 KC4  H2   C13  C29  108.56  3.000
 KC4  H2   C13  N14  107.67  3.000
 KC4  C29  C13  N14  112.21  3.000
 KC4  H2   C13  C12  108.28  3.000
 KC4  N14  C13  C12  109.25  3.000
 KC4  C29  C13  C12  110.75  3.000
 KC4  N17  C15  O16  123.34  3.000
 KC4  N17  C15  N14  113.20  3.000
 KC4  O16  C15  N14  123.46  3.000
 KC4  H3   C20  C19  119.78  3.000
 KC4  H3   C20  C21  120.96  3.000
 KC4  C19  C20  C21  119.26  3.000
 KC4  C27  C21  O22  119.86  3.000
 KC4  O22  C21  C20  119.49  3.000
 KC4  C27  C21  C20  120.57  3.000
 KC4  H4   C28  C27  118.67  3.000
 KC4  H4   C28  C18  121.16  3.000
 KC4  C27  C28  C18  120.17  3.000
 KC4  H7   C01  H6   108.40  3.000
 KC4  H7   C01  H5   108.32  3.000
 KC4  H6   C01  H5   108.21  3.000
 KC4  H7   C01  N02  108.37  3.000
 KC4  H6   C01  N02  112.08  3.000
 KC4  H5   C01  N02  111.36  3.000
 KC4  H8   N02  C03  120.01  3.000
 KC4  H8   N02  C01  117.65  3.000
 KC4  C03  N02  C01  121.97  3.000
 KC4  C32  C05  C06  117.94  3.000
 KC4  C32  C05  C03  123.61  3.000
 KC4  C06  C05  C03  118.42  3.000
 KC4  H9   C06  C07  118.56  3.000
 KC4  H9   C06  C05  119.73  3.000
 KC4  C07  C06  C05  121.71  3.000
 KC4  H10  C07  C08  121.73  3.000
 KC4  H10  C07  C06  118.45  3.000
 KC4  C08  C07  C06  119.81  3.000
 KC4  C31  C08  O09  115.92  3.000
 KC4  O09  C08  C07  125.12  3.000
 KC4  C31  C08  C07  118.96  3.000
 KC4  C08  O09  C10  120.91  3.000
 KC4  H12  C11  H11  107.19  3.000
 KC4  H12  C11  C12  109.57  3.000
 KC4  H11  C11  C12  109.72  3.000
 KC4  H12  C11  C10  109.94  3.000
 KC4  H11  C11  C10  109.36  3.000
 KC4  C12  C11  C10  110.99  3.000
 KC4  H14  C12  H13  106.76  3.000
 KC4  H14  C12  C11  109.52  3.000
 KC4  H13  C12  C11  109.50  3.000
 KC4  H14  C12  C13  109.85  3.000
 KC4  H13  C12  C13  109.48  3.000
 KC4  C11  C12  C13  111.62  3.000
 KC4  H15  N14  C15  118.87  3.000
 KC4  H15  N14  C13  116.44  3.000
 KC4  C15  N14  C13  122.62  3.000
 KC4  H16  N17  C18  114.78  3.000
 KC4  H16  N17  C15  116.87  3.000
 KC4  C18  N17  C15  127.82  3.000
 KC4  C19  C18  N17  117.03  3.000
 KC4  C19  C18  C28  118.52  3.000
 KC4  N17  C18  C28  124.41  3.000
 KC4  H17  C19  C18  119.80  3.000
 KC4  H17  C19  C20  118.94  3.000
 KC4  C18  C19  C20  121.26  3.000
 KC4  H18  C27  C28  119.15  3.000
 KC4  H18  C27  C21  120.62  3.000
 KC4  C28  C27  C21  120.21  3.000
 KC4  H20  C29  H19  106.82  3.000
 KC4  H20  C29  C30  109.88  3.000
 KC4  H19  C29  C30  109.60  3.000
 KC4  H20  C29  C13  109.15  3.000
 KC4  H19  C29  C13  109.83  3.000
 KC4  C30  C29  C13  111.44  3.000
 KC4  H22  C30  H21  106.83  3.000
 KC4  H22  C30  C29  109.86  3.000
 KC4  H21  C30  C29  109.52  3.000
 KC4  H22  C30  C10  108.84  3.000
 KC4  H21  C30  C10  111.29  3.000
 KC4  C29  C30  C10  110.44  3.000
 KC4  H23  C31  C32  120.08  3.000
 KC4  H23  C31  C08  119.42  3.000
 KC4  C32  C31  C08  120.49  3.000
 KC4  H24  C32  C31  117.82  3.000
 KC4  H24  C32  C05  121.09  3.000
 KC4  C31  C32  C05  121.07  3.000
 KC4  C23  O22  C21  117.65  3.000
 KC4  C05  C03  O04  121.23  3.000
 KC4  C05  C03  N02  116.89  3.000
 KC4  O04  C03  N02  121.88  3.000
 KC4  F26  C23  F25  108.34  3.000
 KC4  F25  C23  F24  106.65  3.000
 KC4  F26  C23  F24  108.23  3.000
 KC4  F25  C23  O22  112.84  3.000
 KC4  F26  C23  O22  107.74  3.000
 KC4  F24  C23  O22  112.88  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 KC4  CONST_01  C28  C18  C19  C20    0.00   0.0  0
 KC4  CONST_02  C28  C27  C21  C20    0.00   0.0  0
 KC4  CONST_03  C18  C28  C27  C21    0.00   0.0  0
 KC4  CONST_04  C18  C19  C20  C21    0.00   0.0  0
 KC4  CONST_05  C08  C07  C06  C05    0.00   0.0  0
 KC4  CONST_06  C08  C31  C32  C05    0.00   0.0  0
 KC4  CONST_07  C31  C32  C05  C06    0.00   0.0  0
 KC4  CONST_08  C31  C08  C07  C06    0.00   0.0  0
 KC4  CONST_09  C32  C05  C06  C07    0.00   0.0  0
 KC4  CONST_10  C32  C31  C08  C07    0.00   0.0  0
 KC4  CONST_11  C27  C28  C18  C19    0.00   0.0  0
 KC4  CONST_12  C27  C21  C20  C19    0.00   0.0  0
 KC4  CONST_13  N17  C18  C19  C20  180.00   0.0  0
 KC4  CONST_14  O22  C21  C27  C28  180.00   0.0  0
 KC4  CONST_15  C07  C06  C05  C03  180.00   0.0  0
 KC4  CONST_16  C31  C32  C05  C03  180.00   0.0  0
 KC4  CONST_17  O09  C08  C07  C06  180.00   0.0  0
 KC4  CONST_18  C32  C31  C08  O09  180.00   0.0  0
 KC4  CONST_19  C27  C28  C18  N17  180.00   0.0  0
 KC4  CONST_20  O22  C21  C20  C19  180.00   0.0  0
 KC4  CONST_21  H18  C27  C21  C20  180.00   0.0  0
 KC4  CONST_22  H4   C28  C27  C21  180.00   0.0  0
 KC4  CONST_23  H17  C19  C20  C21  180.00   0.0  0
 KC4  CONST_24  H10  C07  C06  C05  180.00   0.0  0
 KC4  CONST_25  H23  C31  C32  C05  180.00   0.0  0
 KC4  CONST_26  H24  C32  C05  C06  180.00   0.0  0
 KC4  CONST_27  H9   C06  C07  C08  180.00   0.0  0
 KC4  CONST_28  H3   C20  C19  C18  180.00   0.0  0
 KC4  CONST_31  H16  N17  C18  C28  180.00   0.0  0
 KC4  CONST_32  O16  C15  N14  C13    0.00   0.0  0
 KC4  CONST_33  C05  C03  N02  C01  180.00   0.0  0
 KC4  CONST_34  C18  N17  C15  O16    0.00   0.0  0
 KC4  CONST_35  C18  N17  C15  N14  180.00   0.0  0
 KC4  CONST_36  N17  C15  N14  C13  180.00   0.0  0
 KC4  CONST_37  H8   N02  C03  C05    0.00   0.0  0
 KC4  CONST_38  O04  C03  N02  C01    0.00   0.0  0
 KC4  CONST_39  H15  N14  C15  O16  180.00   0.0  0
 KC4  Var_01    C13  C12  C11  C10   55.63  30.0  1
 KC4  Var_02    C13  C29  C30  C10  -56.67  30.0  1
 KC4  Var_03    C07  C08  O09  C10    4.00  30.0  2
 KC4  Var_04    C06  C05  C03  N02  160.98  30.0  2
 KC4  Var_05    C27  C21  O22  C23   90.51  30.0  2
 KC4  Var_06    F24  C23  O22  C21  -61.76  30.0  3
 KC4  Var_07    H5   C01  N02  C03  -57.26  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 KC4  chir_01  C10  O09  C11  C30  positiv
 KC4  chir_02  C13  N14  C12  C29  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 KC4  plan-1  C20  0.020
 KC4  plan-1  C21  0.020
 KC4  plan-1  C28  0.020
 KC4  plan-1  N17  0.020
 KC4  plan-1  C18  0.020
 KC4  plan-1  C19  0.020
 KC4  plan-1  C27  0.020
 KC4  plan-1  H3   0.020
 KC4  plan-1  H4   0.020
 KC4  plan-1  H17  0.020
 KC4  plan-1  H18  0.020
 KC4  plan-1  O22  0.020
 KC4  plan-2  C05  0.020
 KC4  plan-2  C06  0.020
 KC4  plan-2  C07  0.020
 KC4  plan-2  C08  0.020
 KC4  plan-2  O09  0.020
 KC4  plan-2  C31  0.020
 KC4  plan-2  C32  0.020
 KC4  plan-2  H9   0.020
 KC4  plan-2  H10  0.020
 KC4  plan-2  H23  0.020
 KC4  plan-2  H24  0.020
 KC4  plan-2  C03  0.020
 KC4  plan-3  C13  0.020
 KC4  plan-3  C15  0.020
 KC4  plan-3  N14  0.020
 KC4  plan-3  O16  0.020
 KC4  plan-3  N17  0.020
 KC4  plan-3  C18  0.020
 KC4  plan-3  H15  0.020
 KC4  plan-3  H16  0.020
 KC4  plan-4  C01  0.020
 KC4  plan-4  N02  0.020
 KC4  plan-4  O04  0.020
 KC4  plan-4  C05  0.020
 KC4  plan-4  H8   0.020
 KC4  plan-4  C03  0.020

